| Previous changeset 4:a26f0a30df65 (2018-12-14) Next changeset 6:4f55668547fc (2020-01-24) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59 |
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modified:
gemini_gene_wise.xml gemini_macros.xml repository_dependencies.xml test-data/gemini_amend_input.db test-data/gemini_annotate_result.db test-data/gemini_auto_dom_input.db test-data/gemini_auto_rec_input.db test-data/gemini_comphets_input.db test-data/gemini_de_novo_input.db test-data/gemini_is_somatic_result.db test-data/gemini_load_result1.db test-data/gemini_load_result2.db test-data/gemini_versioned_databases.loc test-data/test-cache/gemini-config.yaml |
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added:
test-data/test-cache/gemini/data/clinvar_20170130.tidy.vcf.gz test-data/test-cache/gemini/data/clinvar_20170130.tidy.vcf.gz.tbi test-data/test-cache/gemini/data/dbsnp.b147.20160601.tidy.vcf.gz test-data/test-cache/gemini/data/dbsnp.b147.20160601.tidy.vcf.gz.tbi test-data/test-cache/gemini/data/gnomad.exomes.r2.0.1.sites.no-VEP.nohist.tidy.vcf.gz test-data/test-cache/gemini/data/gnomad.exomes.r2.0.1.sites.no-VEP.nohist.tidy.vcf.gz.tbi |
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removed:
test-data/test-cache/gemini/data/clinvar_20160203.tidy.vcf.gz test-data/test-cache/gemini/data/clinvar_20160203.tidy.vcf.gz.tbi test-data/test-cache/gemini/data/dbsnp.b141.20140813.hg19.tidy.vcf.gz test-data/test-cache/gemini/data/dbsnp.b141.20140813.hg19.tidy.vcf.gz.tbi |
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| diff -r a26f0a30df65 -r 4b26f6c99227 gemini_gene_wise.xml --- a/gemini_gene_wise.xml Fri Dec 14 12:55:02 2018 -0500 +++ b/gemini_gene_wise.xml Fri Jan 11 17:48:39 2019 -0500 |
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| b'@@ -1,5 +1,5 @@\n-<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.1">\n- <description>Custom genotype filtering by gene</description>\n+<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@">\n+ <description>Discover per-gene variant patterns across families</description>\n <macros>\n <import>gemini_macros.xml</import>\n <token name="@BINARY@">gene_wise</token>\n@@ -11,34 +11,62 @@\n <![CDATA[\n gemini @BINARY@\n \n- \n #if int($min_filters) > 0:\n- --min_filters $min_filters\n+ --min-filters $min_filters\n #end if\n \n- #set $multiline_sql_expr = $gt_filter\n- #set $cmdln_param = "--gt-filter"\n- @MULTILN_SQL_EXPR_TO_CMDLN@\n+ #for $filter in $filter_by_genotype:\n+ #set $multiline_sql_expr = str($filter.gt_filter)\n+ #if $filter.is_required:\n+ #set $cmdln_param = "--gt-filter-required"\n+ #else:\n+ #set $cmdln_param = "--gt-filter"\n+ #end if\n+ @MULTILN_SQL_EXPR_TO_CMDLN@\n+ #end for\n \n+ #set $report = $oformat.report\n @COLUMN_SELECT@\n \n- @CMDLN_SQL_FILTER_FILTER_OPTION@\n+ #set $where_clause_elements = []\n+ #set $filter_cmdln_param = \'--filter\'\n+ #for $cond in $constraint:\n+ #if str($cond.filter).strip():\n+ #silent $where_clause_elements.append(str($cond.filter).strip())\n+ #if $cond.overwrite_default_filter:\n+ #set $filter_cmdln_param = \'--where\'\n+ #end if\n+ #end if\n+ #end for\n \n- "${ infile }"\n- > "${ outfile }"\n+ @PARSE_REGION_ELEMENTS@\n+ #if $region_elements:\n+ #silent $where_clause_elements.append(" OR ".join($region_elements))\n+ #end if\n+ #set $filter = " AND ".join($where_clause_elements)\n+ #if str($filter):\n+ $filter_cmdln_param \'$filter\'\n+ #end if\n+\n+ \'$infile\'\n+ > \'$outfile\'\n ]]>\n </command>\n <inputs>\n <expand macro="infile" />\n-\n- <param name="gt_filter" type="text" area="True" size="5x50" label="Restrictions to apply to genotype values" help="(--gt-filter)">\n- <expand macro="sanitize_query" />\n- </param>\n- <param name="min_filters" type="integer" value="0" min="0" label="Minimum number of filters" help="(--min-filters)" />\n- <expand macro="column_filter" />\n- <expand macro="filter" />\n-\n-\n+ <expand macro="gt_filter" default_repeat="1" min_repeat="1" max_repeat="999">\n+ <param name="is_required" type="boolean" checked="False"\n+ label="Make this an obligate filter that a variant has to pass to be considered"\n+ help="By default, a variant has to pass a minimum number of genotype filters (set below) to get reported. By making a filter required, you ensure that variants that fail this one filter are always excluded. Required filters that a variant passes do not count towards its number of passed (regular) filters" />\n+ </expand>\n+ <param name="min_filters" type="integer" value="1" min="1" label="Minimum number of filters" help="(--min-filters)" />\n+ <expand macro="region_filter" />\n+ <expand macro="insert_constraint">\n+ <expand macro="overwritable_where_default" default_where="exonic, high impact variants (SQL clause: is_exonic = 1 and impact_severity != \'LOW\')" />\n+ </expand>\n+ <section name="oformat" title="Output - included information" expanded="true">\n+ <expand macro="column_filter" />\n+ </section>\n </inputs>\n <outputs>\n <data name="outfile" format="tabular" />\n@@ -46,10 +74,12 @@\n <tests>\n <test>\n <param name="'..b'id	gene.*" />\n </assert_contents>\n </output>\n </test>\n@@ -58,7 +88,81 @@\n <![CDATA[\n **What it does**\n \n-The gemini query tool allows querying by variant and the inheritance tools described above enable querying by gene for fixed inheritance patterns. The gene_wise tool allows querying by gene with custom genotype filters to bridge the gap between these tools.\n+This tool extends the *GEMINI inheritance pattern* tool in that it lets you\n+search for custom gene-wise inheritance patterns of variants, instead of fixed\n+ones.\n+\n+See also: the `command line tool documentation\n+<https://gemini.readthedocs.io/en/latest/content/tools.html#gene-wise-custom-genotype-filtering-by-gene>`__\n+\n+-----\n+\n+*Genotype filters*\n+\n+The syntax for specifying a genotype filter (``--gt-filter`` command line\n+option) is the same as for the *GEMINI query* tool and is described `here\n+<https://gemini.readthedocs.io/en/latest/content/querying.html#gt-filter-filtering-on-genotypes>`__.\n+\n+The difference with the *gene_wise* tool is that it lets you specify multiple\n+such filters and, if you do, every filter can be met by a **different variant**\n+as long as all of them are in the **same gene**.\n+\n+This is useful if your analysis includes several families that you suspect\n+(based on a shared phenotype) to have the same gene affected, but not\n+necessarily through the same variant. In this case, you can formulate one filter\n+per family like, for example::\n+\n+ gt_types.fam1_kid == HET and gt_types.fam1_mom == HOM_REF and gt_types.fam1_dad == HOM_REF\n+\n+ gt_types.fam2_kid == HET\n+\n+ gt_types.fam3_kid == HET\n+\n+, which would allow you to find a causal gene that\'s affected by different\n+(dominant) variants in children from three different families. Note that the\n+first filter combines three conditions applied to family 1, which, thus, must\n+be met by the same variant site.\n+\n+*Regular and required filters* (``--gt-filter`` *vs* ``--gt-filter-required``)\n+and the *Minimum number of filters*\n+\n+For every single genotype filter you define you can specify whether it should\n+be applied as a regular or as a required filter. The difference is that, if a\n+variant doesn\'t pass a required filter it is excluded from further analysis.\n+Of the regular filters, a gene and its variants only have to pass a threshold\n+number defined by *Minimum number of filters* (``--min-filters``). Imagine,\n+with the above filters you had specified ``--min-filters`` as ``2``, then a\n+gene for which the child in family 3 carries one copy of a variant allele and\n+the child in family 3 carries a copy of a different allele would be reported\n+no matter if any other allele in that gene passes the first filter, *etc.*.\n+\n+-----\n+\n+*Region filters*\n+\n+They let you restrict your analysis to parts of the genome, which can be useful\n+if you have prior knowledge of the approximate location of the causative gene.\n+\n+If you specify more then one region filter, they get combined with a logical\n+*OR*, meaning variants and genes falling in *any* of the regions are reported.\n+\n+-----\n+\n+*Additional constraints on variants*\n+\n+These get translated directly into the WHERE clause of an SQL query and, thus,\n+have to be expressed in valid SQL syntax. Of particular interest, here, is the\n+fact that, by default, the *gene-wise* tool applies the WHERE clause:\n+``is_exonic = 1 and impact_severity != \'LOW\'``, which means the tool only\n+considers variants in exons that are not of *LOW* impact severity (*i.e.*, not\n+silent mutations). While this can be a good and biologically justifiable\n+setting, you can overwrite it if you need.\n+\n+Note that in SQL syntax tests for equality use a single ``=``, while genotype\n+filters (discussed above) are following Python syntax and use ``==`` for the\n+same purpose. Also note that non-numerical values need to be enclosed in\n+single-quotes, *e.g.* ``\'LOW\'``, but numerical values must *NOT* be.\n+\n ]]>\n </help>\n <expand macro="citations"/>\n' |
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| diff -r a26f0a30df65 -r 4b26f6c99227 gemini_macros.xml --- a/gemini_macros.xml Fri Dec 14 12:55:02 2018 -0500 +++ b/gemini_macros.xml Fri Jan 11 17:48:39 2019 -0500 |
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| b'@@ -1,15 +1,12 @@\n <macros>\n <!-- gemini version to be used -->\n- <token name="@VERSION@">0.18.1</token>\n+ <token name="@VERSION@">0.20.1</token>\n <!-- minimal annotation files version required by this version of gemini -->\n- <token name="@DB_VERSION@">181</token>\n+ <token name="@DB_VERSION@">200</token>\n \n <xml name="requirements">\n <requirements>\n <requirement type="package" version="@VERSION@">gemini</requirement>\n- <requirement type="package" version="0.2.6">tabix</requirement>\n- <!-- for conda useage -->\n- <!--requirement type="package" version="1.3.1">htslib</requirement-->\n <yield />\n </requirements>\n </xml>\n@@ -24,9 +21,17 @@\n <exit_code range=":-1" />\n <regex match="Error:" />\n <regex match="Exception:" />\n+ <yield />\n </stdio>\n </xml>\n \n+ <xml name="citations">\n+ <citations>\n+ <citation type="doi">10.1371/journal.pcbi.1003153</citation>\n+ <yield />\n+ </citations>\n+ </xml>\n+\n <xml name="annotation_dir">\n <param name="annotation_databases" type="select" label="Choose a gemini annotation source">\n <options from_data_table="gemini_versioned_databases">\n@@ -36,31 +41,36 @@\n </param>\n </xml>\n \n- <xml name="add_header_column">\n- <param name="header" type="boolean" truevalue="--header" falsevalue="" checked="False" \n- label="Add a header of column names to the output" help="(--header)"/>\n- </xml>\n-\n- <xml name="radius">\n- <param name="radius" type="integer" value="3" label="Set filter for Breadth-first search (BFS) in the Protein-Protein Interaction network" help="(-r)" >\n- <validator type="in_range" min="0"/>\n+ <xml name="infile">\n+ <param name="infile" type="data" format="gemini.sqlite" label="GEMINI database" help="Only files with version @VERSION@ are accepted." >\n+ <options options_filter_attribute="metadata.gemini_version" >\n+ <filter type="add_value" value="@VERSION@" />\n+ </options>\n </param>\n </xml>\n- <xml name="variant_mode">\n- <param name="variant_mode" type="boolean" truevalue="--var" falsevalue="" checked="False" \n- label="Returns variant info (e.g. impact, biotype) for interacting genes" help="(--var)"/>\n+\n+ <xml name="add_header_column">\n+ <param argument="--header" name="header" type="boolean" truevalue="--header" falsevalue="" checked="True" \n+ label="Add a header of column names to the output" />\n </xml>\n \n- <xml name="column_filter">\n+ <xml name="column_filter" token_help="" token_minimalset="variant_id, gene">\n <conditional name="report">\n- <param name="report_selector" type="select" label="Columns to include in the report"\n- help="By default, this tool reports all columns in the variants table. One may choose to report only a subset of the columns.">\n- <option value="all" selected="True">all</option>\n- <option value="column_filter">User given columns</option>\n+ <param name="report_selector" type="select"\n+ label="Set of columns to include in the variant report table"\n+ help="@HELP@">\n+ <option value="minimal">Minimal (report only a preconfigured minimal set of columns)</option>\n+ <option value="full">Full (report all columns defined in the GEMINI database variants table)</option>\n+ <option value="custom">Custom (report user-specified columns)</option>\n </param>\n- <when value="all"/>\n- <when value="column_filter">\n- <param name="columns" type="select" display="checkboxes" multiple="True" label="Choose columns to include in the report" help="(--columns)">\n+ <when value="full" />\n+ <when value="minimal">\n+ '..b'r($report.extra_cols).strip():\n+ #if $cols:\n+ #set $cols = $cols + \', \' + str($report.extra_cols)\n+ #else:\n+ #set $cols = str($report.extra_cols)\n+ #end if\n+ #end if\n+ #if not $cols:\n+ #set $cols = "variant_id, gene"\n+ #end if\n #end if\n </token>\n \n <token name="@COLUMN_SELECT@">\n- #if $report.report_selector != \'all\':\n- --columns "${report.columns}\n- #if str($report.extra_cols).strip()\n- #echo \',\'+\',\'.join(str($report.extra_cols).split()) \n- #end if\n- "\n+ @SET_COLS@\n+ #if $cols != "*"\n+ --columns \'$cols\'\n #end if\n </token>\n \n- <xml name="family">\n- <param name="families" type="text" value="" label="Comma seperated list of families to restrict the analysis to." help="e.g. Family1,Family3 (--families)"/>\n- </xml>\n-\n- <xml name="lenient">\n- <param name="lenient" type="boolean" truevalue="--lenient" falsevalue="" checked="False" label="Loosen the restrictions on family structure"/>\n- </xml>\n-\n- <xml name="unaffected">\n- <param name="allow_unaffected" type="boolean" truevalue="--allow-unaffected" falsevalue="" checked="False" label="Report candidates that also impact samples labeled as unaffected." help="(--allow-unaffected)"/>\n- </xml>\n-\n- <xml name="min_kindreds">\n- <param name="min_kindreds" type="integer" value="1" label="The min. number of kindreds that must have a candidate variant in a gene" help="default: 1 (--min-kindreds)" />\n- </xml>\n-\n- <xml name="min_sequence_depth">\n- <param name="d" type="integer" value="0" min="0" label="The minimum aligned sequence depth (genotype DP) required for each sample"\n- help="default: 0 (-d)" />\n- </xml>\n-\n- <xml name="min_gq">\n- <param name="min_gq" type="integer" value="0" label="the minimum genotype quality required for each sample in a family" help="default: 0 (--min-gq)">\n- <validator type="in_range" min="0"/>\n- </param>\n- </xml>\n-\n- <xml name="gt_pl_max">\n- <param name="gt_pl_max" type="integer" value="-1" min="-1" label="The maximum phred-scaled genotype likelihod (PL) allowed for each sample in a family" help="default: -1 (not set) (--gt-pl-max)" />\n- </xml>\n-\n- <xml name="citations">\n- <citations>\n- <citation type="doi">10.1371/journal.pcbi.1003153</citation>\n- <yield />\n- </citations>\n- </xml>\n-\n- <xml name="infile">\n- <param name="infile" type="data" format="gemini.sqlite" label="GEMINI database" help="Only files with version @VERSION@ are accepted." >\n- <options options_filter_attribute="metadata.gemini_version" >\n- <filter type="add_value" value="@VERSION@" />\n- </options>\n- <validator type="expression" message="This version of Gemini will only work with Gemini files that are for version @VERSION@.">value is not None and value.metadata.gemini_version == "@VERSION@"</validator>\n- </param>\n- </xml>\n-\n+ <token name="@PARSE_REGION_ELEMENTS@"><![CDATA[\n+ #set $region_elements = []\n+ #for $r in $regions:\n+ ## The actual chromosome name needs to be single-quoted\n+ ## in SQL, so we need to quote the single quotes like the\n+ ## sanitize_query macro would if the whole was a parameter.\n+ #set $r_elements = ["chrom = \'\\"\'\\"\'%s\'\\"\'\\"\'" % str($r.chrom).strip()]\n+ #if str($r.start).strip():\n+ #silent $r_elements.append("start >= %d" % int($r.start))\n+ #end if\n+ #if str($r.stop).strip():\n+ #silent $r_elements.append("end <= %d" % int($r.stop))\n+ #end if\n+ #silent $region_elements.append("(%s)" % " AND ".join($r_elements))\n+ #end for\n+ ]]>\n+ </token>\n </macros>\n' |
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| diff -r a26f0a30df65 -r 4b26f6c99227 repository_dependencies.xml --- a/repository_dependencies.xml Fri Dec 14 12:55:02 2018 -0500 +++ b/repository_dependencies.xml Fri Jan 11 17:48:39 2019 -0500 |
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| @@ -1,4 +1,4 @@ <?xml version="1.0" ?> <repositories description="This requires the GEMINI data manager definition to install all required annotation databases."> - <repository changeset_revision="fe5a9a7d95b0" name="data_manager_gemini_database_downloader" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"/> + <repository changeset_revision="f57426daa04d" name="data_manager_gemini_database_downloader" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"/> </repositories> \ No newline at end of file |
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| diff -r a26f0a30df65 -r 4b26f6c99227 test-data/gemini_versioned_databases.loc --- a/test-data/gemini_versioned_databases.loc Fri Dec 14 12:55:02 2018 -0500 +++ b/test-data/gemini_versioned_databases.loc Fri Jan 11 17:48:39 2019 -0500 |
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| @@ -1,3 +1,3 @@ ## GEMINI versioned databases #DownloadDate dbkey DBversion Description Path -1999-01-01 hg19 181 GEMINI annotations (test snapshot) ${__HERE__}/test-cache +1999-01-01 hg19 200 GEMINI annotations (test snapshot) ${__HERE__}/test-cache |
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| diff -r a26f0a30df65 -r 4b26f6c99227 test-data/test-cache/gemini-config.yaml --- a/test-data/test-cache/gemini-config.yaml Fri Dec 14 12:55:02 2018 -0500 +++ b/test-data/test-cache/gemini-config.yaml Fri Jan 11 17:48:39 2019 -0500 |
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| @@ -2,12 +2,14 @@ versions: ALL.wgs.phase3_shapeit2_mvncall_integrated_v5a.20130502.sites.tidy.vcf.gz: 4 ESP6500SI.all.snps_indels.tidy.v2.vcf.gz: 2 - ExAC.r0.3.sites.vep.tidy.vcf.gz: 3 + ExAC.r0.3.sites.vep.tidy.vcf.gz: 4 GRCh37-gms-mappability.vcf.gz: 2 - clinvar_20160203.tidy.vcf.gz: 5 + clinvar_20170130.tidy.vcf.gz: 5 cosmic-v68-GRCh37.tidy.vcf.gz: 3 - dbsnp.b141.20140813.hg19.tidy.vcf.gz: 4 + dbsnp.b147.20160601.tidy.vcf.gz: 1 detailed_gene_table_v75: 2 geno2mp.variants.tidy.vcf.gz: 1 + gnomad.exomes.r2.0.1.sites.no-VEP.nohist.tidy.vcf.gz: 2 hg19.rmsk.bed.gz: 2 summary_gene_table_v75: 2 + whole_genome_SNVs.tsv.compressed.gz: 2 |
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